I have a problem and I haven't solved yet: I have 3 computers with a Intel DB75EN motherboard. In one of them I have to install 2 identical network cards (PCI-E x1). Motherboard has 2 PCI, 1 PCI-E x1 and 1 PCI-E x16, so I have installed one card in PCI-E x1 and the other one in PCI-E x16.
Here is where my problem starts: only card installed in PCI-E x1 is detected by BIOS. I changed position between cards, I tried in one of the other identical PC, but behavior is always the same: not working in PCI-E x16.
Finally, I have tried with both network cards in different motherboards with PCI-E x16 and it works!
I don't think my motherboard should be incompatible for this purpose. I have checked Intel page, and there is a page called "Tested Peripherals", where are mentioned some x4 cards, who should have been connected to x16 port